@jbrowse/plugin-comparative-adapters 2.17.0 → 3.0.0

package/esm/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.js

@@ -1,9 +1,9 @@
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { openLocation } from '@jbrowse/core/util/io';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { doesIntersect2 } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
-import { readFile, parseBed } from '../util';
+import { parseBed, readFile } from '../util';
 class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
     async setup(opts) {
         if (!this.setupP) {
@@ -51,9 +51,6 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
         };
     }
     async hasDataForRefName() {
-        // determining this properly is basically a call to getFeatures
-        // so is not really that important, and has to be true or else
-        // getFeatures is never called (BaseFeatureDataAdapter filters it out)
         return true;
     }
     getAssemblyNames() {
@@ -62,7 +59,6 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
     }
     async getRefNames(opts = {}) {
         var _a;
-        // @ts-expect-error
         const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
         const { feats } = await this.setup(opts);
         const idx = this.getAssemblyNames().indexOf(r1);
@@ -86,8 +82,6 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
     getFeatures(region, opts = {}) {
         return ObservableCreate(async (observer) => {
             const { assemblyNames, feats } = await this.setup(opts);
-            // The index of the assembly name in the region list corresponds to
-            // the adapter in the subadapters list
             const index = assemblyNames.indexOf(region.assemblyName);
             if (index !== -1) {
                 const flip = index === 0;
@@ -127,12 +121,7 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the foreseeable future and can be purged
-     * from caches, etc
-     */
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }
 MCScanAnchorsAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default MCScanAnchorsAdapter;

package/esm/MCScanSimpleAnchorsAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const MCScanSimpleAnchorsAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     mcscanSimpleAnchorsLocation: {
         type: string;
         defaultValue: {
@@ -9,9 +6,6 @@ declare const MCScanSimpleAnchorsAdapter: import("@jbrowse/core/configuration/co
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     bed1Location: {
         type: string;
         defaultValue: {
@@ -19,9 +13,6 @@ declare const MCScanSimpleAnchorsAdapter: import("@jbrowse/core/configuration/co
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     bed2Location: {
         type: string;
         defaultValue: {
@@ -29,9 +20,6 @@ declare const MCScanSimpleAnchorsAdapter: import("@jbrowse/core/configuration/co
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: string;
         defaultValue: never[];

package/esm/MCScanSimpleAnchorsAdapter/configSchema.js

@@ -1,12 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config MCScanSimpleAnchorsAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const MCScanSimpleAnchorsAdapter = ConfigurationSchema('MCScanSimpleAnchorsAdapter', {
-    /**
-     * #slot
-     */
     mcscanSimpleAnchorsLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -14,9 +8,6 @@ const MCScanSimpleAnchorsAdapter = ConfigurationSchema('MCScanSimpleAnchorsAdapt
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     bed1Location: {
         type: 'fileLocation',
         defaultValue: {
@@ -24,9 +15,6 @@ const MCScanSimpleAnchorsAdapter = ConfigurationSchema('MCScanSimpleAnchorsAdapt
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     bed2Location: {
         type: 'fileLocation',
         defaultValue: {
@@ -34,9 +22,6 @@ const MCScanSimpleAnchorsAdapter = ConfigurationSchema('MCScanSimpleAnchorsAdapt
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],

package/esm/MCScanSimpleAnchorsAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function MCScanSimpleAnchorsAdapterF(pluginManager: PluginManager): void;

package/esm/MCScanSimpleAnchorsAdapter/index.js

@@ -6,7 +6,7 @@ export default function MCScanSimpleAnchorsAdapterF(pluginManager) {
         displayName: 'MCScan anchors.simple adapter',
         configSchema,
         adapterMetadata: {
-            hiddenFromGUI: true,
+            category: 'Synteny adapters',
         },
         getAdapterClass: () => import('./MCScanSimpleAnchorsAdapter').then(r => r.default),
     }));

package/esm/MashMapAdapter/MashMapAdapter.d.ts

@@ -1,5 +1,5 @@
-import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import PAFAdapter from '../PAFAdapter/PAFAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 export default class MashMapAdapter extends PAFAdapter {
     setupPre(opts?: BaseOptions): Promise<{
         tname: string;

package/esm/MashMapAdapter/MashMapAdapter.js

@@ -1,5 +1,5 @@
-import { openLocation } from '@jbrowse/core/util/io';
 import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
 import PAFAdapter from '../PAFAdapter/PAFAdapter';
 import { parseLineByLine } from '../util';
 export default class MashMapAdapter extends PAFAdapter {
@@ -12,7 +12,6 @@ export default class MashMapAdapter extends PAFAdapter {
 function parseMashMapLine(line) {
     const fields = line.split(' ');
     if (fields.length < 9) {
-        // xref https://github.com/marbl/MashMap/issues/38
         throw new Error(`improperly formatted line: ${line}`);
     }
     const [qname, , qstart, qend, strand, tname, , tstart, tend, mq] = fields;

package/esm/MashMapAdapter/configSchema.d.ts

@@ -1,31 +1,19 @@
 declare const MashMapAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: string;
         defaultValue: never[];
         description: string;
     };
-    /**
-     * #slot
-     */
     targetAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     queryAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     outLocation: {
         type: string;
         defaultValue: {

package/esm/MashMapAdapter/configSchema.js

@@ -1,36 +1,21 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config MashMapAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const MashMapAdapter = ConfigurationSchema('MashMapAdapter', {
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],
         description: 'Array of assembly names to use for this file. The query assembly name is the first value in the array, target assembly name is the second',
     },
-    /**
-     * #slot
-     */
     targetAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames array: the target assembly',
     },
-    /**
-     * #slot
-     */
     queryAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames array: the query assembly',
     },
-    /**
-     * #slot
-     */
     outLocation: {
         type: 'fileLocation',
         defaultValue: {

package/esm/MashMapAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function MashMapAdapterF(pluginManager: PluginManager): void;

package/esm/MashMapAdapter/index.js

@@ -6,7 +6,7 @@ export default function MashMapAdapterF(pluginManager) {
         displayName: 'MashMap adapter',
         configSchema,
         adapterMetadata: {
-            hiddenFromGUI: true,
+            category: 'Synteny adapters',
         },
         getAdapterClass: () => import('./MashMapAdapter').then(r => r.default),
     }));

package/esm/PAFAdapter/PAFAdapter.d.ts

@@ -1,8 +1,9 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { PAFRecord } from './util';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { PAFRecord } from './util';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature } from '@jbrowse/core/util';
+import type { Region } from '@jbrowse/core/util/types';
 interface PAFOptions extends BaseOptions {
     config?: AnyConfigurationModel;
 }

package/esm/PAFAdapter/PAFAdapter.js

@@ -1,13 +1,12 @@
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { doesIntersect2 } from '@jbrowse/core/util/range';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
+import { doesIntersect2 } from '@jbrowse/core/util/range';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
-import { readConfObject, } from '@jbrowse/core/configuration';
 import { MismatchParser } from '@jbrowse/plugin-alignments';
-// locals
 import SyntenyFeature from '../SyntenyFeature';
-import { flipCigar, swapIndelCigar, parsePAFLine, parseLineByLine, } from '../util';
+import { flipCigar, parseLineByLine, parsePAFLine, swapIndelCigar, } from '../util';
 import { getWeightedMeans } from './util';
 const { parseCigar } = MismatchParser;
 class PAFAdapter extends BaseFeatureDataAdapter {
@@ -27,9 +26,6 @@ class PAFAdapter extends BaseFeatureDataAdapter {
         return parseLineByLine(buf, parsePAFLine);
     }
     async hasDataForRefName() {
-        // determining this properly is basically a call to getFeatures so is not
-        // really that important, and has to be true or else getFeatures is never
-        // called (BaseAdapter filters it out)
         return true;
     }
     getAssemblyNames() {
@@ -43,7 +39,6 @@ class PAFAdapter extends BaseFeatureDataAdapter {
     }
     async getRefNames(opts = {}) {
         var _a;
-        // @ts-expect-error
         const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
         const feats = await this.setup(opts);
         const idx = this.getAssemblyNames().indexOf(r1);
@@ -61,18 +56,12 @@ class PAFAdapter extends BaseFeatureDataAdapter {
         return ObservableCreate(async (observer) => {
             let pafRecords = await this.setup(opts);
             const { config } = opts;
-            // note: this is not the adapter config, it is responding to a display
-            // setting passed in via the opts parameter
             if (config && readConfObject(config, 'colorBy') === 'meanQueryIdentity') {
                 pafRecords = getWeightedMeans(pafRecords);
             }
             const assemblyNames = this.getAssemblyNames();
-            // The index of the assembly name in the query list corresponds to the
-            // adapter in the subadapters list
             const { start: qstart, end: qend, refName: qref, assemblyName } = query;
             const index = assemblyNames.indexOf(assemblyName);
-            // if the getFeatures::query is on the query assembly, flip orientation
-            // of data
             const flip = index === 0;
             if (index === -1) {
                 console.warn(`${assemblyName} not found in this adapter`);
@@ -140,7 +129,7 @@ class PAFAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources( /* { query } */) { }
+    freeResources() { }
 }
 PAFAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default PAFAdapter;

package/esm/PAFAdapter/configSchema.d.ts

@@ -1,31 +1,19 @@
 declare const PAFAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: string;
         defaultValue: never[];
         description: string;
     };
-    /**
-     * #slot
-     */
     targetAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     queryAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     pafLocation: {
         type: string;
         defaultValue: {

package/esm/PAFAdapter/configSchema.js

@@ -1,36 +1,21 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config PAFAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const PAFAdapter = ConfigurationSchema('PAFAdapter', {
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],
         description: 'Array of assembly names to use for this file. The query assembly name is the first value in the array, target assembly name is the second',
     },
-    /**
-     * #slot
-     */
     targetAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames: the target assembly name',
     },
-    /**
-     * #slot
-     */
     queryAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames: the query assembly name',
     },
-    /**
-     * #slot
-     */
     pafLocation: {
         type: 'fileLocation',
         defaultValue: {

package/esm/PAFAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function PAFAdapterF(pluginManager: PluginManager): void;

package/esm/PAFAdapter/index.js

@@ -6,7 +6,7 @@ export default function PAFAdapterF(pluginManager) {
         displayName: 'PAF adapter',
         configSchema,
         adapterMetadata: {
-            hiddenFromGUI: true,
+            category: 'Synteny adapters',
         },
         getAdapterClass: () => import('./PAFAdapter').then(r => r.default),
     }));

package/esm/PAFAdapter/util.js

@@ -1,38 +1,4 @@
 import { zip } from '../util';
-// based on "weighted mean" method from https://github.com/tpoorten/dotPlotly
-// License reproduced here
-//
-// MIT License
-// Copyright (c) 2017 Tom Poorten
-// Permission is hereby granted, free of charge, to any person obtaining a copy
-// of this software and associated documentation files (the "Software"), to deal
-// in the Software without restriction, including without limitation the rights
-// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-// copies of the Software, and to permit persons to whom the Software is
-// furnished to do so, subject to the following conditions:
-// The above copyright notice and this permission notice shall be included in all
-// copies or substantial portions of the Software.
-// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-// SOFTWARE.
-//
-// Notes: in the weighted mean longer alignments factor in more heavily of all
-// the fragments of a query vs the reference that it mapped to
-//
-// this uses a combined key query+'-'+ref to iteratively map all the alignments
-// that match a particular ref from a particular query (so 1d array of what
-// could be a 2d map)
-//
-// the result is a single number that says e.g. chr5 from human mapped to chr5
-// on mouse with 0.8 quality, and that0.8 is then attached to all the pieces of
-// chr5 on human that mapped to chr5 on mouse. if chr5 on human also more
-// weakly mapped to chr6 on mouse, then it would have another value e.g. 0.6.
-// this can show strong and weak levels of synteny, especially in polyploidy
-// situations
 export function getWeightedMeans(ret) {
     const scoreMap = {};
     for (const entry of ret) {
@@ -67,7 +33,6 @@ export function getWeightedMeans(ret) {
     }
     return ret;
 }
-// https://gist.github.com/stekhn/a12ed417e91f90ecec14bcfa4c2ae16a
 function weightedMean(tuples) {
     const [valueSum, weightSum] = tuples.reduce(([valueSum, weightSum], [value, weight]) => [
         valueSum + value * weight,

package/esm/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.d.ts

@@ -1,10 +1,11 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import PluginManager from '@jbrowse/core/PluginManager';
 import { TabixIndexedFile } from '@gmod/tabix';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import type { Feature } from '@jbrowse/core/util';
+import type { Region } from '@jbrowse/core/util/types';
 interface PAFOptions extends BaseOptions {
     config?: AnyConfigurationModel;
 }

package/esm/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.js

@@ -1,10 +1,9 @@
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { openLocation } from '@jbrowse/core/util/io';
 import { TabixIndexedFile } from '@gmod/tabix';
-// locals
-import { parsePAFLine } from '../util';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import SyntenyFeature from '../SyntenyFeature';
+import { parsePAFLine } from '../util';
 class PAFAdapter extends BaseFeatureDataAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
@@ -93,12 +92,12 @@ class PAFAdapter extends BaseFeatureDataAdapter {
                         },
                     }));
                 },
-                signal: opts.signal,
+                stopToken: opts.stopToken,
             });
             observer.complete();
         });
     }
-    freeResources( /* { query } */) { }
+    freeResources() { }
 }
 PAFAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default PAFAdapter;

package/esm/PairwiseIndexedPAFAdapter/configSchema.d.ts

@@ -1,31 +1,19 @@
 declare const PairwiseIndexedPAFAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: string;
         defaultValue: never[];
         description: string;
     };
-    /**
-     * #slot
-     */
     targetAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     queryAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     pifGzLocation: {
         type: string;
         description: string;
@@ -34,21 +22,12 @@ declare const PairwiseIndexedPAFAdapter: import("@jbrowse/core/configuration/con
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: import("mobx-state-tree").ISimpleType<string>;
             type: string;
             defaultValue: string;
         };
-        /**
-         * #slot index.location
-         */
         location: {
             type: string;
             defaultValue: {

package/esm/PairwiseIndexedPAFAdapter/configSchema.js

@@ -1,37 +1,22 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { types } from 'mobx-state-tree';
-/**
- * #config PairwiseIndexedPAFAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const PairwiseIndexedPAFAdapter = ConfigurationSchema('PairwiseIndexedPAFAdapter', {
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],
         description: 'Array of assembly names to use for this file. The query assembly name is the first value in the array, target assembly name is the second',
     },
-    /**
-     * #slot
-     */
     targetAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames: the target assembly name',
     },
-    /**
-     * #slot
-     */
     queryAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames: the query assembly name',
     },
-    /**
-     * #slot
-     */
     pifGzLocation: {
         type: 'fileLocation',
         description: 'location of pairwise tabix indexed PAF (pif)',
@@ -40,21 +25,12 @@ const PairwiseIndexedPAFAdapter = ConfigurationSchema('PairwiseIndexedPAFAdapter
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     index: ConfigurationSchema('TabixIndex', {
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: types.enumeration('IndexType', ['TBI', 'CSI']),
             type: 'stringEnum',
             defaultValue: 'TBI',
         },
-        /**
-         * #slot index.location
-         */
         location: {
             type: 'fileLocation',
             defaultValue: {

package/esm/PairwiseIndexedPAFAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function PairwiseIndexedPAFAdapterF(pluginManager: PluginManager): void;

package/esm/PairwiseIndexedPAFAdapter/index.js

@@ -6,7 +6,7 @@ export default function PairwiseIndexedPAFAdapterF(pluginManager) {
         displayName: 'Pairwise indexed PAF adapter',
         configSchema,
         adapterMetadata: {
-            hiddenFromGUI: true,
+            category: 'Synteny adapters',
         },
         getAdapterClass: () => import('./PairwiseIndexedPAFAdapter').then(r => r.default),
     }));

package/esm/SyntenyFeature/index.js

@@ -1,6 +1,5 @@
 import { SimpleFeature } from '@jbrowse/core/util';
 import { MismatchParser } from '@jbrowse/plugin-alignments';
-// locals
 const { getMismatches } = MismatchParser;
 export default class SyntenyFeature extends SimpleFeature {
     get(arg) {